FMODB ID: 8586Y
Calculation Name: 4BXT-B-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 4BXT
Chain ID: B
UniProt ID: Q91KZ5
Base Structure: X-ray
Registration Date: 2023-06-21
Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.
Modeling method
Optimization | MOE:Amber10:EHT |
---|---|
Restraint | OptH |
Protonation | MOE:Protonate 3D |
Complement | MOE:Structure Preparation |
Water | No |
Procedure | Auto-FMO protocol ver. 2.20220422 |
FMO calculation
FMO method | FMO2-MP2/6-31G(d) |
---|---|
Fragmentation | Auto |
Number of fragment | 25 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -75377.00613 |
---|---|
FMO2-HF: Nuclear repulsion | 65401.336662 |
FMO2-HF: Total energy | -9975.669468 |
FMO2-MP2: Total energy | -10004.480341 |
3D Structure
Ligand structure
Ligand Interaction
Ligand binding energy
"IFIE [kcal/mol] | PIEDA [kcal/mol] | Charge transfer value [e] | |||
---|---|---|---|---|---|
IFIE SUMIFIE SUM at MP2 level. | ESElectro static interaction energy. | EXExchange-repulsion energy. | CT+mixCharge transfer and mixing terms energy. | DI(MP2)Dispersion energy. | q(I=>J)Charge transfer value from I to J fragments. |
N/A | N/A | N/A | N/A | N/A | N/A |
Interactive mode: IFIE and PIEDA for fragment #1(B:170:LEU)
Summations of interaction energy for
fragment #1(B:170:LEU)
IFIE [kcal/mol] | PIEDA [kcal/mol] | Charge transfer value [e] | |||
---|---|---|---|---|---|
IFIE SUMIFIE SUM at MP2 level. | ESElectro static interaction energy. | EXExchange-repulsion energy. | CT+mixCharge transfer and mixing terms energy. | DI(MP2)Dispersion energy. | q(I=>J)Charge transfer value from I to J fragments. |
-2.22 | 0.253 | 4.052 | -2.065 | -4.461 | -0.004 |
Interaction energy analysis for fragmet #1(B:170:LEU)
frag_NumFragment number. | ChainChain species. | Res #Residue number. | RES3-letter code of amino acid residue, ligand and solvent molecule. | FCHARGEFormal charge [e]. | q_MullikenFragment charge evaluated by Mulliken charge [e]. | q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. | DISTDistance from Ligand [Å]. | TotalIFIE at MP2 level [kcal/mol]. | ESElectro static interaction energy by PIEDA [kcal/mol]. | EXExchange-repulsion energy by PIEDA [kcal/mol]. | CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. | DI(MP2)Dispersion energy by PIEDA [kcal/mol]. | q(I=>J)Charge transfer value from I to J fragmens [e]. |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
3 | B | 172 | ILE | 0 | 0.029 | -0.010 | 3.632 | -1.892 | -0.513 | 0.003 | -0.593 | -0.790 | 0.002 |
4 | B | 173 | GLU | -1 | -0.905 | -0.947 | 6.066 | -0.416 | -0.416 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | B | 174 | ALA | 0 | 0.078 | 0.048 | 2.059 | -0.350 | -0.662 | 2.927 | -0.895 | -1.720 | -0.006 |
6 | B | 175 | ARG | 1 | 0.883 | 0.941 | 2.348 | 0.585 | 1.867 | 1.123 | -0.564 | -1.841 | 0.000 |
7 | B | 176 | LEU | 0 | -0.022 | -0.030 | 4.460 | 0.135 | 0.259 | -0.001 | -0.013 | -0.110 | 0.000 |
8 | B | 177 | GLU | -1 | -0.900 | -0.932 | 6.582 | -0.758 | -0.758 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | B | 178 | SER | 0 | -0.025 | -0.012 | 4.830 | 0.186 | 0.186 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | B | 179 | ILE | 0 | -0.054 | -0.035 | 6.920 | 0.155 | 0.155 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | B | 180 | GLU | -1 | -0.951 | -0.972 | 9.357 | -0.309 | -0.309 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | B | 181 | GLU | -1 | -0.906 | -0.946 | 9.647 | -0.506 | -0.506 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | B | 182 | LYS | 1 | 0.934 | 0.952 | 8.038 | 0.558 | 0.558 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | B | 183 | LEU | 0 | 0.000 | -0.003 | 12.472 | 0.052 | 0.052 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | B | 184 | SER | 0 | 0.050 | 0.026 | 15.120 | 0.048 | 0.048 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | B | 185 | MET | 0 | -0.051 | -0.007 | 14.270 | 0.023 | 0.023 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | B | 186 | ILE | 0 | -0.001 | 0.000 | 15.248 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | B | 187 | LEU | 0 | 0.011 | -0.002 | 18.568 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | B | 188 | GLY | 0 | -0.019 | -0.009 | 20.234 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | B | 189 | LEU | 0 | 0.011 | -0.002 | 18.610 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | B | 190 | LEU | 0 | 0.000 | 0.035 | 22.334 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | B | 191 | ARG | 1 | 0.931 | 0.977 | 24.358 | 0.149 | 0.149 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | B | 192 | THR | 0 | -0.076 | -0.080 | 25.444 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | B | 193 | LEU | 0 | -0.042 | -0.009 | 25.914 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | B | 194 | ASN | 0 | -0.045 | -0.006 | 29.529 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |